CRISPR-U™ Gene Knockout Cell Line
Strategy
SMARCA4 Gene Knockout Strategy
CRISPR-U™ technology (CRISPR based), developed by Ubigene, is more efficient than general
CRISPR/Cas9 technology in double-strand breaking and homologous recombination. With CRISPR-U™, Ubigene has
successfully edited over 3000 genes on more than 100 types of cell lines.
Objective
To create a Human SMARCA4 Knockout
model in cell line by
CRISPR-U™-mediated
genome
engineering.
Target gene info 
| Official symbol | SMARCA4 |
| Gene id | 6597 |
| Organism | Homo sapiens |
| Official full symbol | SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 |
| Gene type | protein-coding |
| Also known as | BAF190, BAF190A, BRG1, CSS4, MRD16, RTPS2, SNF2, SNF2-beta, SNF2L4, SNF2LB, SWI2, hSNF2b |
| Summary | The protein encoded by this gene is a member of the SWI/SNF family of proteins and is similar to the brahma protein of Drosophila. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein is part of the large ATP-dependent chromatin remodeling complex SNF/SWI, which is required for transcriptional activation of genes normally repressed by chromatin. In addition, this protein can bind BRCA1, as well as regulate the expression of the tumorigenic protein CD44. Mutations in this gene cause rhabdoid tumor predisposition syndrome type 2. Multiple transcript variants encoding different isoforms have been found for this gene. |
| Genomic regions | Chromosome 19 |
Strategy Summary
This gene has 36 protein coding transcripts：
| Name | Transcript ID | bp | Protein | Biotype | CCDS | UniProt Match | RefSeq Match | Flags |
| SMARCA4-235 | ENST00000644737.1 | 5777 | 1617aa | Protein coding | CCDS45972 | P51532-4 | - | GENCODE basic, |
| SMARCA4-215 | ENST00000590574.6 | 5739 | 1614aa | Protein coding | CCDS54217 | P51532-2 | - | TSL:5, GENCODE basic, |
| SMARCA4-203 | ENST00000429416.8 | 5665 | 1647aa | Protein coding | CCDS12253 | P51532-1 | - | TSL:2, GENCODE basic, APPRIS P1, |
| SMARCA4-246 | ENST00000646510.1 | 5595 | 1614aa | Protein coding | CCDS54217 | P51532-2 | - | GENCODE basic, |
| SMARCA4-245 | ENST00000646484.1 | 5579 | 1614aa | Protein coding | CCDS54217 | P51532-2 | - | GENCODE basic, |
| SMARCA4-201 | ENST00000344626.10 | 5577 | 1647aa | Protein coding | CCDS12253 | P51532-1 | NM_003072.5 | TSL:1, GENCODE basic, APPRIS P1, MANE Select v0.92, |
| SMARCA4-225 | ENST00000643296.1 | 5563 | 1617aa | Protein coding | CCDS45972 | P51532-4 | - | GENCODE basic, |
| SMARCA4-253 | ENST00000647230.1 | 5554 | 1614aa | Protein coding | CCDS54217 | P51532-2 | - | GENCODE basic, |
| SMARCA4-241 | ENST00000645460.1 | 5457 | 1613aa | Protein coding | CCDS54218 | P51532-5 | - | GENCODE basic, |
| SMARCA4-204 | ENST00000444061.8 | 5393 | 1613aa | Protein coding | CCDS54218 | P51532-5 | - | TSL:5, GENCODE basic, |
| SMARCA4-214 | ENST00000589677.5 | 5181 | 1616aa | Protein coding | CCDS45973 | P51532-3 | - | TSL:5, GENCODE basic, |
| SMARCA4-207 | ENST00000541122.6 | 5139 | 1617aa | Protein coding | CCDS45972 | P51532-4 | - | TSL:5, GENCODE basic, |
| SMARCA4-249 | ENST00000646693.1 | 5774 | 1679aa | Protein coding | - | Q9HBD4 | - | GENCODE basic, |
| SMARCA4-223 | ENST00000642726.1 | 5675 | 1646aa | Protein coding | - | A0A2R8Y7S2 | - | GENCODE basic, |
| SMARCA4-222 | ENST00000642628.1 | 5637 | 1646aa | Protein coding | - | A0A2R8Y7S2 | - | GENCODE basic, |
| SMARCA4-227 | ENST00000643549.1 | 5609 | 1649aa | Protein coding | - | A0A2R8Y4P4 | - | GENCODE basic, |
| SMARCA4-202 | ENST00000413806.7 | 5512 | 1681aa | Protein coding | - | A0A0A0MT49 | - | TSL:5, GENCODE basic, |
| SMARCA4-205 | ENST00000450717.7 | 5506 | 1679aa | Protein coding | - | Q9HBD4 | - | TSL:5, GENCODE basic, |
| SMARCA4-216 | ENST00000591545.6 | 5192 | 1165aa | Protein coding | - | A0A2R8YGP5 | - | CDS 5' incomplete, TSL:2, |
| SMARCA4-230 | ENST00000643995.1 | 4817 | 1455aa | Protein coding | - | A0A2R8YGG3 | - | CDS 5' incomplete, |
| SMARCA4-237 | ENST00000644963.1 | 4045 | 1198aa | Protein coding | - | A0A2R8YG32 | - | CDS 5' incomplete, |
| SMARCA4-224 | ENST00000643208.1 | 3940 | 1165aa | Protein coding | - | A0A2R8Y7F3 | - | CDS 5' incomplete, |
| SMARCA4-231 | ENST00000644065.1 | 3802 | 1192aa | Protein coding | - | A0A2R8Y440 | - | CDS 5' incomplete, |
| SMARCA4-220 | ENST00000642350.1 | 3750 | 1145aa | Protein coding | - | A0A2R8Y6N0 | - | CDS 5' incomplete, |
| SMARCA4-250 | ENST00000646746.1 | 3680 | 1081aa | Protein coding | - | A0A2R8Y7Y7 | - | CDS 5' incomplete, |
| SMARCA4-228 | ENST00000643857.1 | 3637 | 1068aa | Protein coding | - | A0A2R8Y526 | - | CDS 5' incomplete, |
| SMARCA4-254 | ENST00000647268.1 | 3522 | 1065aa | Protein coding | - | A0A2R8YF58 | - | CDS 5' incomplete, |
| SMARCA4-243 | ENST00000646183.1 | 3496 | 1094aa | Protein coding | - | A0A2R8YF80 | - | CDS 5' incomplete, |
| SMARCA4-226 | ENST00000643534.1 | 3426 | 1041aa | Protein coding | - | A0A2R8Y6V2 | - | CDS 5' incomplete, |
| SMARCA4-221 | ENST00000642508.1 | 2612 | 799aa | Protein coding | - | A0A2R8Y523 | - | CDS 5' incomplete, |
| SMARCA4-212 | ENST00000586985.2 | 1968 | 348aa | Protein coding | - | K7EQF0 | - | CDS 5' incomplete, TSL:5, |
| SMARCA4-239 | ENST00000645236.1 | 1887 | 522aa | Protein coding | - | A0A2R8Y5K3 | - | CDS 5' incomplete, |
| SMARCA4-247 | ENST00000646513.1 | 1127 | 375aa | Protein coding | - | A0A2R8YFV8 | - | CDS 5' and 3' incomplete, |
| SMARCA4-206 | ENST00000538456.4 | 1108 | 336aa | Protein coding | - | A0A2R8YFK5 | - | CDS 5' incomplete, TSL:3, |
| SMARCA4-218 | ENST00000592158.2 | 911 | 221aa | Protein coding | - | K7EP28 | - | CDS 5' incomplete, TSL:2, |
| SMARCA4-236 | ENST00000644760.1 | 740 | 157aa | Protein coding | - | A0A2R8Y866 | - | CDS 3' incomplete, |
| SMARCA4-234 | ENST00000644327.1 | 4237 | 1047aa | Nonsense mediated decay | - | A0A2R8Y4C5 | - | CDS 5' incomplete, |
| SMARCA4-238 | ENST00000645061.1 | 4035 | 985aa | Nonsense mediated decay | - | A0A2R8YDA1 | - | CDS 5' incomplete, |
| SMARCA4-233 | ENST00000644290.1 | 3355 | 192aa | Nonsense mediated decay | - | A0A2R8Y7R0 | - | CDS 5' incomplete, |
| SMARCA4-242 | ENST00000645648.1 | 3250 | 385aa | Nonsense mediated decay | - | A0A2R8YCY3 | - | CDS 5' incomplete, |
| SMARCA4-248 | ENST00000646593.1 | 3206 | 55aa | Nonsense mediated decay | - | A0A2R8Y583 | - | CDS 5' incomplete, |
| SMARCA4-244 | ENST00000646236.1 | 2802 | 234aa | Nonsense mediated decay | - | A0A2R8Y4R6 | - | CDS 5' incomplete, |
| SMARCA4-240 | ENST00000645387.1 | 627 | 58aa | Nonsense mediated decay | - | A0A2R8YF38 | - | CDS 5' incomplete, |
| SMARCA4-211 | ENST00000586921.1 | 569 | No protein | Processed transcript | - | - | - | TSL:5, |
| SMARCA4-209 | ENST00000586122.5 | 512 | No protein | Processed transcript | - | - | - | TSL:5, |
| SMARCA4-208 | ENST00000585799.5 | 3842 | No protein | Retained intron | - | - | - | TSL:2, |
| SMARCA4-232 | ENST00000644267.1 | 3382 | No protein | Retained intron | - | - | - | - |
| SMARCA4-217 | ENST00000591595.5 | 3377 | No protein | Retained intron | - | - | - | TSL:2, |
| SMARCA4-219 | ENST00000592604.6 | 3358 | No protein | Retained intron | - | - | - | TSL:1, |
| SMARCA4-229 | ENST00000643929.1 | 1865 | No protein | Retained intron | - | - | - | - |
| SMARCA4-251 | ENST00000646889.1 | 1659 | No protein | Retained intron | - | - | - | - |
| SMARCA4-210 | ENST00000586892.1 | 559 | No protein | Retained intron | - | - | - | TSL:4, |
| SMARCA4-213 | ENST00000587988.5 | 552 | No protein | Retained intron | - | - | - | TSL:2, |
| SMARCA4-252 | ENST00000647011.1 | 487 | No protein | Retained intron | - | - | - | - |
Red Cotton™ Assessment
Project Difficulty Level unknown
| Target Gene | SMARCA4 |
| This KO Strategy | loading |
| Red Cotton™ Notes | Gene SMARCA4 had been KO in hek293t cell line. |
Aforementioned information comes from Ubigene database. Different origin of cell lines may have
different condition. Ubigene reserved all the right for final explanation.
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Work flow
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